Variants of CRISPR from Prevotella and Francisella 1 (Cpf1)

ABSTRACT

Engineered CRISPR from  Prevotella  and  Francisella  1 (Cpf1) nucleases with altered and improved target specificity and their use in genomic engineering, epigenomic engineering, genome targeting, genome editing, and in vitro diagnostics.

CLAIM OF PRIORITY

This application claims the benefit of U.S. Patent Application Ser. No. 62/366,976, filed on Jul. 26, 2016. The entire contents of the foregoing are hereby incorporated by reference.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under Grant No. GM105378 awarded by the National Institutes of Health. The Government has certain rights in the invention.

TECHNICAL FIELD

The invention relates, at least in part, to engineered CRISPR from Prevotella and Francisella 1 (Cpf1) nucleases with altered and improved target specificity and their use in genomic engineering, epigenomic engineering, genome targeting, genome editing, and in vitro diagnostics.

BACKGROUND

CRISPR systems enable efficient genome editing in a wide variety of organisms and cell types. The genome-wide specificity of engineered nucleases, including those derived from CRISPR bacterial immune systems such as Cas9 and Cpf1, is of utmost importance when considering such tools for both research and therapeutic applications.

SUMMARY

As described herein, Cpf1 Proteins can be engineered to show increased specificity, theoretically by reducing the binding affinity of Cpf1 for DNA. Thus, described herein are a number of Cpf1 variants, e.g., from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, respectively), that have been engineered to exhibit increased specificity (i.e., induce substantially fewer off target effects) as compared to the wild type protein, as well as methods of using them.

In a first aspect, the invention provides isolated Lachnospiraceae bacterium ND2006 Cpf1 (LbCpf1) proteins, with one or more mutations listed in Table 1, e.g., with mutations at one, two, three, four, five, six or all seven of the following positions: S202, N274, N278, K290, K367, K532, K609, K915, Q962, K963, K966, K1002 and/or S1003, e.g., comprising a sequence that is at least 80% identical to the amino acid sequence of at least amino acids 23-1246 SEQ ID NO:1 (or at least amino acids 18- of SEQ ID NO:1) with mutations at one, two, three, four, five, six, or seven of the following positions S202, N274, N278, K290, K367, K532, K609, K915, Q962, K963, K966, K1002 and/or S1003, and optionally one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag. A mutation alters the amino acid to an amino acid other than the native amino acid (e.g., 497 is anything but N). In preferred embodiments the mutation changes the amino acid to any amino acid other than the native one, arginine or lysine; in some embodiments, the amino acid is alanine.

In some embodiments, the variant LbCpf1 proteins comprise one, two, three, or all four of the following mutations: S202A, N274A, N278A, K290A, K367A, K532A, K609A, K915A, Q962A, K963A, K966A, K1002A and/or S1003A.

In some embodiments, the variant LbCpf1 proteins also comprise one or more mutations that decrease nuclease activity selected from the group consisting of mutations listed in Table A, e.g., mutations at D832 and/or E925, e.g., D832A and E925A.

Also provided herein are isolated Acidaminococcus sp. BV3L6 Cpf1 (AsCpf1) proteins, with one or more mutations listed in Table 1, e.g., with mutations at one, two, three, four, five, or six of the following positions: N178, N278, N282, R301, T315, S376, N515, K523, K524, K603, K965, Q1013, and/or K1054, e.g., comprising a sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:2 with mutations at one, two, three, four, or five, or six of the following positions: N178, N278, N282, R301, T315, S376, N515, K523, K524, K603, K965, Q1013, and/or K1054, and optionally one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag. In some embodiments, the AsCpf1 variants described herein include the amino acid sequence of SEQ ID NO:2, with mutations at one, two, three, four, five, or all six of the following positions: N178A, N278A, N282A, R301A, T315A, S376A, N515A, K523A, K524A, K603A, K965A, Q1013A, and/or K1054A.

In some embodiments, the variant AsCpf1 proteins also comprise one or more mutations that decrease nuclease activity selected from the group consisting of mutations listed in Table A, e.g., mutations at D908 and/or E993, e.g., D908A and/or E993A.

Also provided herein are fusion proteins comprising the isolated variant Cpf1 proteins described herein fused to a heterologous functional domain, with an optional intervening linker, wherein the linker does not interfere with activity of the fusion protein. In preferred embodiments, the heterologous functional domain acts on DNA or protein, e.g., on chromatin. In some embodiments, the heterologous functional domain is a transcriptional activation domain. In some embodiments, the transcriptional activation domain is from VP64 or NF-κB p65. In some embodiments, the heterologous functional domain is a transcriptional silencer or transcriptional repression domain. In some embodiments, the transcriptional repression domain is a Kruppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3A interaction domain (SID). In some embodiments, the transcriptional silencer is Heterochromatin Protein 1 (HP1), e.g., HP1α or HP1β. In some embodiments, the heterologous functional domain is an enzyme that modifies the methylation state of DNA. In some embodiments, the enzyme that modifies the methylation state of DNA is a DNA methyltransferase (DNMT) or the entirety or the dioxygenase domain of a TET protein, e.g., a catalytic module comprising the cysteine-rich extension and the 2OGFeDO domain encoded by 7 highly conserved exons, e.g., the Tet1 catalytic domain comprising amino acids 1580-2052, Tet2 comprising amino acids 1290-1905 and Tet3 comprising amino acids 966-1678. In some embodiments, the TET protein or TET-derived dioxygenase domain is from TET1. In some embodiments, the heterologous functional domain is an enzyme that modifies a histone subunit. In some embodiments, the enzyme that modifies a histone subunit is a histone acetyltransferase (HAT), histone deacetylase (HDAC), histone methyltransferase (HMT), or histone demethylase. In some embodiments, the heterologous functional domain is a biological tether. In some embodiments, the biological tether is MS2, Csy4 or lambda N protein. In some embodiments, the heterologous functional domain is FokI.

Also provided herein are nucleic acids, isolated nucleic acids encoding the variant Cpf1 proteins described herein, as well as vectors comprising the isolated nucleic acids, optionally operably linked to one or more regulatory domains for expressing the variant Cpf1 proteins described herein. Also provided herein are host cells, e.g., bacterial, yeast, insect, or mammalian host cells or transgenic animals (e.g., mice), comprising the nucleic acids described herein, and optionally expressing the variant Cpf1 proteins described herein.

Also provided herein are methods of altering the genome of a cell, by expressing in the cell isolated variant Cpf1 proteins as described herein, in the presence of at least one guide RNA having a region complementary to a selected portion of the genome of the cell with optimal nucleotide spacing at the genomic target site.

Also provided herein are methods of altering the genome of a cell, by expressing in the cell an isolated variant Cpf1 protein described herein, in the presence of at least one guide RNA having a region complementary to a selected portion of the genome of the cell with optimal nucleotide spacing at the genomic target site.

Also provided herein are isolated nucleic acids encoding the Cpf1 variants, as well as vectors comprising the isolated nucleic acids, optionally operably linked to one or more regulatory domains for expressing the variants, and host cells, e.g., mammalian host cells, comprising the nucleic acids, and optionally expressing the variant proteins.

Also provided herein are methods for altering, e.g., selectively altering, the genome of a cell by contacting the cell with, or expressing in the cell, a variant protein as described herein, and a guide RNA having a region complementary to a selected portion of the genome of the cell. In some embodiments, the isolated protein or fusion protein comprises one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.

Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims.

DESCRIPTION OF DRAWINGS

FIGS. 1A-B are bar graphs showing tolerance of AsCpf1 and LbCpf1 to mismatched crRNAs for DNMT1 sites 1 and 3. (A, B) Endogenous gene modification by AsCpf1 and LbCpf1 using crRNAs that contain pairs of mismatched bases (1A) or singly mismatched bases (1B). Activity determined by T7E1 assay; error bars, s.e.m.; n=3.

FIGS. 2A-B are bar graphs showing tolerance of LbCpf1 (2A) and AsCpf1 (2B) to singly mismatched crRNAs for DNMT1 site 7. Endogenous gene modification by AsCpf1 and LbCpf1 determined by T7E1 assay; n=1; n.d., not determined.

FIG. 3 is a bar graph showing wild-type LbCpf1 and alanine substitution variant activity with matched and singly mismatched crRNAs for DNMT1 site 1. Endogenous gene modification determined by T7E1 assay; n=1.

FIG. 4 is a bar graph showing wild-type LbCpf1 and alanine substitution variant activity with matched and singly mismatched crRNAs for DNMT1 site 3. Endogenous gene modification determined by T7E1 assay; n=1; error bars, s.e.m. for n=2.

FIG. 5A-B are bar graphs showing wild-type AsCpf1 and alanine substitution variant activity with matched and singly mismatched crRNAs for DNMT1 site 1. Panels A and B are from separate experiments. Endogenous gene modification determined by T7E1 assay; n=1.

FIG. 6 is a bar graph showing wild-type AsCpf1 and alanine substitution variant activity with matched and singly mismatched crRNAs for DNMT1 site 3. Endogenous gene modification determined by T7E1 assay; n=1.

DETAILED DESCRIPTION

The on- and off-target activities of two CRISPR-Cas Cpf1 orthologues from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, respectively) were recently characterized; see Kleinstiver & Tsai et al., “Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells,” Nature Biotechnology 2016 Jun. 27. doi: 10.1038/nbt.3620, Epub ahead of print). Using crRNAs with intentionally mismatched positions (to mimic mismatched off-target sites) and an unbiased genome-wide detection assay named GUIDE-seq (Tsai et al., Nat Biotechnol 33, 187-197 (2015)), it was determined that both AsCpf1 and LbCpf1 have generally high genome-wide specificities but can still tolerate nucleotide mismatches in parts of the crRNA.

Thus, to generate variants with higher fidelity (i.e., less likelihood of binding to target sites with one or more mismatches, like the Streptococcus pyogenes Cas9 variants (SpCas9-HF) described in Kleinstiver et al., Nature 529, 490-495 (2016)), we made site directed mutations in the Cpf1 coding sequence to improve their genome-wide specificities. The site directed mutations in residues that presumably make contacts to the DNA-backbone of either the target or non-target DNA strand are meant to improve the fidelity of the enzymes by imparting a heightened ability to discriminate against off-target sites. We have identified a number of mutations that can provide such an effect. These studies are performed on AsCpf1 and LbCpf1, enzymes whose specificities have not yet been altered. Importantly, because the Cas9 and Cpf1 enzymes are substantially different at both the primary amino acid sequence level and in their three-dimensional domain organization and structures, it is not at all obvious which amino acid change(s) will be needed to create high-fidelity versions of Cpf1 enzymes. Furthermore, while a crystal structure has been solved for AsCpf1 providing insight into which residues to mutate, for LbCpf1 we are identifying residues to mutate based on alignment with other Cpf1 orthologues.

These higher fidelity Cpf1 (Cpf1-HF) enzymes are useful in both research and therapeutic settings, e.g., for genomic engineering, epigenomic engineering, genome targeting, and genome editing (for example, if you can target an allele with single nucleotide precision, then you can target either the wild-type (reference genome) sequence or the disease allele. This would allow genotyping at disease loci). Methods for using Cpf1 enzymes are known in the art, see, e.g., Yamano et al., Cell. 2016 May 5; 165(4):949-62; Fonfara et al., Nature. 2016 Apr. 28; 532(7600):517-21; Dong et al., Nature. 2016 Apr. 28; 532(7600):522-6; and Zetsche et al., Cell. 2015 Oct. 22; 163(3):759-71.

Cpf1

Clustered, regularly interspaced, short palindromic repeat (CRISPR) systems encode RNA-guided endonucleases that are essential for bacterial adaptive immunity (Wright et al., Cell 164, 29-44 (2016)). CRISPR-associated (Cas) nucleases can be readily programmed to cleave target DNA sequences for genome editing in various organisms²⁻⁵. One class of these nucleases, referred to as Cas9 proteins, complex with two short RNAs: a crRNA and a trans-activating crRNA (tracrRNA)^(7, 8). The most commonly used Cas9 ortholog, SpCas9, uses a crRNA that has 20nucleotides (nt) at its 5′ end that are complementary to the “protospacer” region of the target DNA site. Efficient cleavage also requires that SpCas9 recognizes a protospacer adjacent motif (PAM). The crRNA and tracrRNA are usually combined into a single ˜100-nt guide RNA (gRNA)^(7, 9-11) that directs the DNA cleavage activity of SpCas9. The genome-wide specificities of SpCas9 nucleases paired with different gRNAs have been characterized using many different approaches¹²⁻¹⁵. SpCas9 variants with substantially improved genome-wide specificities have also been engineered^(16, 17).

Recently, a Cas protein named Cpf1 has been identified that can also be programmed to cleave target DNA sequences^(1, 18-20). Unlike SpCas9, Cpf1 requires only a single 42-nt crRNA, which has 23 nt at its 3′ end that are complementary to the protospacer of the target DNA sequence′. Furthermore, whereas SpCas9 recognizes an NGG PAM sequence that is 3′ of the protospacer, AsCpf1 and LbCp1 recognize TTTN PAMs that are found 5′ of the protospacer¹. Early experiments with AsCpf1 and LbCpf1 showed that these nucleases can be programmed to edit target sites in human cells¹ but they were tested on only a small number of sites. On-target activities and genome-wide specificities of both AsCpf1 and LbCpf1 were characterized in Kleinstiver & Tsai et al., Nature Biotechnology 2016.

The present findings provide support for AsCpf1 and LbCpf1 variants, referred to collectively herein as “variants” or “the variants”.

All of the variants described herein can be rapidly incorporated into existing and widely used vectors, e.g., by simple site-directed mutagenesis.

Thus, provided herein are Cpf1 variants, including LbCpf1 variants. The LbCpf1 wild type protein sequence is as follows:

Type V CRISPR-associated protein Cpfl [Lachnospiraceae bacterium ND2006], GenBank AccNo. WP_051666128.1 (SEQ ID NO: 1)

  61 RAEDYKGVKK LLDRYYLSFI NDVLHSIKLK NLNNYISLFR KKTRTEKENK ELENLEINLR  121 KEIAKAFKGN EGYKSLFKKD IIETILPEFL DDKDEIALVN SFNGFTTAFT GFFDNRENMF  181 SEEAKSTSIA FRCINENLTR YISNMDIFEK VDAIFDKHEV QEIKEKILNS DYDVEDFFEG  241 EFFNFVLTQE GIDVYNAIIG GFVTESGEKI KGLNEYINLY NQKTKQKLPK FKPLYKQVLS  301 DRESLSFYGE GYTSDEEVLE VFRNTLNKNS EIFSSIKKLE KLFKNFDEYS SAGIFVKNGP  361 AISTISKDIF GEWNVIRDKW NAEYDDIHLK KKAVVTEKYE DDRRKSFKKI GSFSLEQLQE  421 YADADLSVVE KLKEIIIQKV DEIYKVYGSS EKLFDADFVL EKSLKKNDAV VAIMKDLLDS  481 VKSFENYIKA FFGEGKETNR DESFYGDFVL AYDILLKVDH IYDAIRNYVT QKPYSKDKFK  541 LYFQNPQFMG GWDKDKETDY RATILRYGSK YYLAIMDKKY AKCLQKIDKD DVNGNYEKIN  601 YKLLPGPNKM LPKVFFSKKW MAYYNPSEDI QKIYKNGTFK KGDMFNLNDC HKLIDFFKDS  661 ISRYPKWSNA YDFNFSETEK YKDIAGFYRE VEEQGYKVSF ESASKKEVDK LVEEGKLYMF  721 QIYNKDFSDK SHGTPNLHTM YFKLLFDENN HGQIRLSGGA ELFMRRASLK KEELVVHPAN  781 SPIANKNPDN PKKTTTLSYD VYKDKRFSED QYELHIPIAI NKCPKNIFKI NTEVRVLLKH  841 DDNPYVIGID RGERNLLYIV VVDGKGNIVE QYSLNEIINN FNGIRIKTDY HSLLDKKEKE  901 RFEARQNWTS IENIKELKAG YISQVVHKIC ELVEKYDAVI ALEDLNSGFK NSRVKVEKQV  961 YQKFEKMLID KLNYMVDKKS NPCATGGALK GYQITNKFES FKSMSTQNGF IFYIPAWLTS 1021 KIDPSTGFVN LLKIKYTSIA DSKKFISSFD RIMYVPEEDL FEFALDYKNF SRTDADYIKK 1081 WKLYSYGNRI RIFRNPKKNN VFDWEEVCLT SAYKELFNKY GINYQQGDIR ALLCEQSDKA 1141 FYSSFMALMS LMLQMRNSIT GRTDVDFLIS PVKNSDGIFY DSRNYEAQEN AILPKNADAN 1201 GAYNIARKVL WAIGQFKKAE DEKLDKVKIA ISNKEWLEYA QTSVKH

The LbCpf1 variants described herein can include the amino acid sequence of SEQ ID NO:1, e.g., at least comprising amino acids 23-1246 of SEQ ID NO:1, with mutations (i.e., replacement of the native amino acid with a different amino acid, e.g., alanine, glycine, or serine), at one or more positions in Table 1, e.g., at the following positions: S186, N256, N260, K272, K349, K514, K591, K897, Q944, K945, K948, K984, and/or S985 of SEQ ID NO:10 (or at positions analogous thereto, e.g., S202, N274, N278, K290, K367, K532, K609, K915, Q962, K963, K966, K1002, and/or S1003 of SEQ ID NO:1); amino acids 19-1246 of SEQ ID NO:1 are identical to amino acids 1-1228 of SEQ ID NO:10 (amino acids 1-1228 of SEQ ID NO:10 are referred to herein as LbCPF1 (−18)). In some embodiments, the LbCpf1 variants are at least 80%, e.g., at least 85%, 90%, or 95% identical to the amino acid sequence of SEQ ID NO:1, e.g., have differences at up to 5%, 10%, 15%, or 20% of the residues of SEQ ID NO:1 replaced, e.g., with conservative mutations, in addition to the mutations described herein. In preferred embodiments, the variant retains desired activity of the parent, e.g., the nuclease activity (except where the parent is a nickase or a dead Cpf1), and/or the ability to interact with a guide RNA and target DNA). The version of LbCpf1 used in the present working examples starts at the MSKLEK motif, omitting the first 18 amino acids boxed above as described in Zetsche et al. Cell 163, 759-771 (2015).

Type V CRISPR-associated protein Cpf1 [Acidaminococcus sp. BV3L6], NCBI Reference Sequence: WP_021736722.1 (SEQ ID NO: 2)    1 MTQFEGFTNL YQVSKTLRFE LIPQGKTLKH IQEQGFIEED KARNDHYKEL KPIIDRIYKT   61 YADQCLQLVQ LDWENLSAAI DSYRKEKTEE TRNALIEEQA TYRNAIHDYF IGRIDNLIDA  121 INKRHAEIYK GLFKAELFNG KVLKQLGTVT TTEHENALLR SFDKFTTYFS GFYENRKNVF  181 SAEDISTAIP HRIVQDNFPK FKENCHIFTR LITAVPSLRE HFENVKKAIG IFVSTSIEEV  241 FSFPFYNQLL TQTQIDLYNQ LLGGISREAG TEKIKGLNEV LNLAIQKNDE TAHIIASLPH  301 RFIPLFKQIL SDRNTLSFIL EEFKSDEEVI QSFCKYKTLL RNENVLETAE ALFNELNSID  361 LTHIFISHKK LETISSALCD HWDTLRNALY ERRISELTGK ITKSAKEKVQ RSLKHEDINL  421 QEIISAAGKE LSEAFKQKTS EILSHAHAAL DQPLPTTLKK QEEKEILKSQ LDSLLGLYHL  481 LDWFAVDESN EVDPEFSARL TGIKLEMEPS LSFYNKARNY ATKKPYSVEK FKLNFQMPTL  541 ASGWDVNKEK NNGAILFVKN GLYYLGIMPK QKGRYKALSF EPTEKTSEGF DKMYYDYFPD  601 AAKMIPKCST QLKAVTAHFQ THTTPILLSN NFIEPLEITK EIYDLNNPEK EPKKFQTAYA  661 KKTGDQKGYR EALCKWIDFT RDFLSKYTKT TSIDLSSLRP SSQYKDLGEY YAELNPLLYH  721 ISFQRIAEKE IMDAVETGKL YLFQIYNKDF AKGHHGKPNL HTLYWTGLFS PENLAKTSIK  781 LNGQAELFYR PKSRMKRMAH RLGEKMLNKK LKDQKTPIPD TLYQELYDYV NHRLSHDLSD  841 EARALLPNVI TKEVSHEIIK DRRFTSDKFF FHVPITLNYQ AANSPSKFNQ RVNAYLKEHP  901 ETPIIGIDRG ERNLIYITVI DSTGKILEQR SLNTIQQFDY QKKLDNREKE RVAARQAWSV  961 VGTIKDLKQG YLSQVIHEIV DLMIHYQAVV VLENLNFGFK SKRTGIAEKA VYQQFEKMLI 1021 DKLNCLVLKD YPAEKVGGVL NPYQLTDQFT SFAKMGTQSG FLFYVPAPYT SKIDPLTGFV 1081 DPFVWKTIKN HESRKHFLEG FDFLHYDVKT GDFILHFKMN RNLSFQRGLP GFMPAWDIVF 1141 EKNETQFDAK GTPFIAGKRI VPVIENHRFT GRYRDLYPAN ELIALLEEKG IVFRDGSNIL 1201 PKLLENDDSH AIDTMVALIR SVLQMRNSNA ATGEDYINSP VRDLNGVCFD SRFQNPEWPM 1261 DADANGAYHI ALKGQLLLNH LKESKDLKLQ NGISNQDWLA YIQELRN

The AsCpf1 variants described herein can include the amino acid sequence of SEQ ID NO:2, e.g., at least comprising amino acids 1-1307 of SEQ ID NO:2, with mutations (i.e., replacement of the native amino acid with a different amino acid, e.g., alanine, glycine, or serine (except where the native amino acid is serine)), at one or more positions in Table 1, e.g., at the following positions: N178, S186, N278, N282, R301, T315, S376, N515, K523, K524, K603, K965, Q1013, Q1014, and/or K1054 of SEQ ID NO:2 (or at positions analogous thereto, e.g., of SEQ ID NO:8). In some embodiments, the AsCpf1 variants are at least 80%, e.g., at least 85%, 90%, or 95% identical to the amino acid sequence of SEQ ID NO:2, e.g., have differences at up to 5%, 10%, 15%, or 20% of the residues of SEQ ID NO:2 replaced, e.g., with conservative mutations, in addition to the mutations described herein. In preferred embodiments, the variant retains desired activity of the parent, e.g., the nuclease activity (except where the parent is a nickase or a dead Cpf1), and/or the ability to interact with a guide RNA and target DNA).

To determine the percent identity of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The length of a reference sequence aligned for comparison purposes is at least 80% of the length of the reference sequence, and in some embodiments is at least 90% or 100%. The nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein nucleic acid “identity” is equivalent to nucleic acid “homology”). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences. Percent identity between two polypeptides or nucleic acid sequences is determined in various ways that are within the skill in the art, for instance, using publicly available computer software such as Smith Waterman Alignment (Smith, T. F. and M. S. Waterman (1981) J Mol Biol 147:195-7); “BestFit” (Smith and Waterman, Advances in Applied Mathematics, 482-489 (1981)) as incorporated into GeneMatcher Plus™, Schwarz and Dayhof (1979) Atlas of Protein Sequence and Structure, Dayhof, M. O., Ed, pp 353-358; BLAST program (Basic Local Alignment Search Tool; (Altschul, S. F., W. Gish, et al. (1990) J Mol Biol 215: 403-10), BLAST-2, BLAST-P, BLAST-N, BLAST-X, WU-BLAST-2, ALIGN, ALIGN-2, CLUSTAL, or Megalign (DNASTAR) software. In addition, those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the length of the sequences being compared. In general, for proteins or nucleic acids, the length of comparison can be any length, up to and including full length (e.g., 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 100%). For purposes of the present compositions and methods, at least 80% of the full length of the sequence is aligned.

For purposes of the present invention, the comparison of sequences and determination of percent identity between two sequences can be accomplished using a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.

Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.

In some embodiments, the mutants have alanine in place of the wild type amino acid. In some embodiments, the mutants have any amino acid other than arginine or lysine (or the native amino acid).

In some embodiments, the Cpf1 variants also include one of the following mutations listed in Table A, which reduce or destroy the nuclease activity of the Cpf1:

TABLE A Residues involved in DNA and RNA catalysis AsCpf1 LbCpf1 LbCpf1 (−18) FnCpf1 DNA targeting D908 D850 D832 D917 E911 E853 E835 E920 N913 N855 N837 H922 Y916 Y858 Y840 Y925 E993 E943 E925 E1006 R1226 R1156 R1138 R1218 S1228 S1158 S1140 S1220 D1235 D1166 D1148 D1227 D1263 D1198 D1180 D1255 RNA processing H800 H777 H759 H843 K809 K786 K768 K852 K860 K803 K785 K869 F864 F807 F789 F873 Mutations that turn Cpf1 into a nickase R1226A R1156A R1138A R1218A See, e.g., Yamano et al., Cell. 2016 May 5; 165(4):949-62; Fonfara et al., Nature. 2016 Apr. 28; 532(7600):517-21; Dong et al., Nature. 2016 Apr. 28; 532(7600):522-6; and Zetsche et al., Cell. 2015 Oct. 22; 163(3):759-71. Note that “LbCpf1 (−18)” refers to the sequence of LbCpf1 in Zetsche et al., also shown herein as amino acids 1-1228 of SEQ ID NO:10 and amino acids 19-1246 of SEQ ID NO:1.

Thus, in some embodiments, for AsCpf1, catalytic activity-destroying mutations are made at D908 and E993, e.g., D908A and E993A; and for LbCpf1 catalytic activity-destroying mutations at D832 and E925, e.g., D832A and E925A.

Also provided herein are isolated nucleic acids encoding the Cpf1 variants, vectors comprising the isolated nucleic acids, optionally operably linked to one or more regulatory domains for expressing the variant proteins, and host cells, e.g., mammalian host cells, comprising the nucleic acids, and optionally expressing the variant proteins.

The variants described herein can be used for altering the genome of a cell; the methods generally include expressing the variant proteins in the cells, along with a guide RNA having a region complementary to a selected portion of the genome of the cell. Methods for selectively altering the genome of a cell are known in the art, see, e.g., U.S. Pat. No. 8,993,233; US 20140186958; U.S. Pat. No. 9,023,649; WO/2014/099744; WO 2014/089290; WO2014/144592; WO144288; WO2014/204578; WO2014/152432; WO2115/099850; U.S. Pat. No. 8,697,359; US20160024529; US20160024524; US20160024523; US20160024510; US20160017366; US20160017301; US20150376652; US20150356239; US20150315576; US20150291965; US20150252358; US20150247150; US20150232883; US20150232882; US20150203872; US20150191744; US20150184139; US20150176064; US20150167000; US20150166969; US20150159175; US20150159174; US20150093473; US20150079681; US20150067922; US20150056629; US20150044772; US20150024500; US20150024499; US20150020223; US20140356867; US20140295557; US20140273235; US20140273226; US20140273037; US20140189896; US20140113376; US20140093941; US20130330778; US20130288251; US20120088676; US20110300538; US20110236530; US20110217739; US20110002889; US20100076057; US20110189776; US20110223638; US20130130248; US20150050699; US20150071899; US20150045546; US20150031134; US20150024500; US20140377868; US20140357530; US20140349400; US20140335620; US20140335063; US20140315985; US20140310830; US20140310828; US20140309487; US20140304853; US20140298547; US20140295556; US20140294773; US20140287938; US20140273234; US20140273232; US20140273231; US20140273230; US20140271987; US20140256046; US20140248702; US20140242702; US20140242700; US20140242699; US20140242664; US20140234972; US20140227787; US20140212869; US20140201857; US20140199767; US20140189896; US20140186958; US20140186919; US20140186843; US20140179770; US20140179006; US20140170753; WO/2008/108989; WO/2010/054108; WO/2012/164565; WO/2013/098244; WO/2013/176772; Makarova et al., “Evolution and classification of the CRISPR-Cas systems” 9(6) Nature Reviews Microbiology 467-477 (1-23) (June 2011); Wiedenheft et al., “RNA-guided genetic silencing systems in bacteria and archaea” 482 Nature 331-338 (Feb. 16, 2012); Gasiunas et al., “Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria” 109(39) Proceedings of the National Academy of Sciences USA E2579-E2586 (Sep. 4, 2012); Jinek et al., “A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity” 337 Science 816-821 (Aug. 17, 2012); Carroll, “A CRISPR Approach to Gene Targeting” 20(9) Molecular Therapy 1658-1660 (September 2012); U.S. Appl. No. 61/652,086, filed May 25, 2012; Al-Attar et al., Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs): The Hallmark of an Ingenious Antiviral Defense Mechanism in Prokaryotes, Biol Chem. (2011) vol. 392, Issue 4, pp. 277-289; Hale et al., Essential Features and Rational Design of CRISPR RNAs That Function With the Cas RAMP Module Complex to Cleave RNAs, Molecular Cell, (2012) vol. 45, Issue 3, 292-302.

The variant proteins described herein can be used in place of or in addition to any of the Cas9 or Cpf1 proteins described in the foregoing references, or in combination with analogous mutations described therein. When replacing the Cas9, of course a guide RNA appropriate for the selected Cpf1 is used. In addition, the variants described herein can be used in fusion proteins in place of the wild-type Cas9 or other Cas9 mutations (such as the dCas9 or Cas9 nickase) as known in the art, e.g., a fusion protein with a heterologous functional domains as described in U.S. Pat. No. 8,993,233; US 20140186958; U.S. Pat. No. 9,023,649; WO/2014/099744; WO 2014/089290; WO2014/144592; WO144288; WO2014/204578; WO2014/152432; WO2115/099850; U.S. Pat. No. 8,697,359; US2010/0076057; US2011/0189776; US2011/0223638; US2013/0130248; WO/2008/108989; WO/2010/054108; WO/2012/164565; WO/2013/098244; WO/2013/176772; US20150050699; US 20150071899 and WO 2014/124284. For example, the variants, preferably comprising one or more nuclease-reducing or killing mutation, can be fused on the N or C terminus of the Cpf1 to a transcriptional activation domain or other heterologous functional domains (e.g., transcriptional repressors (e.g., KRAB, ERD, SID, and others, e.g., amino acids 473-530 of the ets2 repressor factor (ERF) repressor domain (ERD), amino acids 1-97 of the KRAB domain of KOX1, or amino acids 1-36 of the Mad mSIN3 interaction domain (SID); see Beerli et al., PNAS USA 95:14628-14633 (1998)) or silencers such as Heterochromatin Protein 1 (HP1, also known as swi6), e.g., HP1α or HP1β; proteins or peptides that could recruit long non-coding RNAs (lncRNAs) fused to a fixed RNA binding sequence such as those bound by the MS2 coat protein, endoribonuclease Csy4, or the lambda N protein; enzymes that modify the methylation state of DNA (e.g., DNA methyltransferase (DNMT) or TET proteins); or enzymes that modify histone subunits (e.g., histone acetyltransferases (HAT), histone deacetylases (HDAC), histone methyltransferases (e.g., for methylation of lysine or arginine residues) or histone demethylases (e.g., for demethylation of lysine or arginine residues)) as are known in the art can also be used. A number of sequences for such domains are known in the art, e.g., a domain that catalyzes hydroxylation of methylated cytosines in DNA. Exemplary proteins include the Ten-Eleven-Translocation (TET)1-3 family, enzymes that converts 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) in DNA.

Sequences for human TET1-3 are known in the art and are shown in the following table:

GenBank Accession Nos. Gene Amino Acid Nucleic Acid TET1 NP_085128.2 NM_030625.2 TET2* NP_001120680.1(var 1) NM_001127208.2 NP_060098.3(var 2) NM_017628.4 TET3 NP_659430.1 NM_144993.1 *Variant (1) represents the longer transcript and encodes the longer isoform (a). Variant (2) differs in the 5′ UTR and in the 3′ UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.

In some embodiments, all or part of the full-length sequence of the catalytic domain can be included, e.g., a catalytic module comprising the cysteine-rich extension and the 2OGFeDO domain encoded by 7 highly conserved exons, e.g., the Tet1 catalytic domain comprising amino acids 1580-2052, Tet2 comprising amino acids 1290-1905 and Tet3 comprising amino acids 966-1678. See, e.g., FIG. 1 of Iyer et al., Cell Cycle. 2009 Jun. 1; 8(11):1698-710. Epub 2009 Jun. 27, for an alignment illustrating the key catalytic residues in all three Tet proteins, and the supplementary materials thereof (available at ftp site ftp.ncbi.nih.gov/pub/aravind/DONS/supplementary_material_DONS.html) for full length sequences (see, e.g., seq 2c); in some embodiments, the sequence includes amino acids 1418-2136 of Tet1 or the corresponding region in Tet2/3.

Other catalytic modules can be from the proteins identified in Iyer et al., 2009.

In some embodiments, the heterologous functional domain is a biological tether, and comprises all or part of (e.g., DNA binding domain from) the MS2 coat protein, endoribonuclease Csy4, or the lambda N protein. These proteins can be used to recruit RNA molecules containing a specific stem-loop structure to a locale specified by the dCpf1 gRNA targeting sequences. For example, a dCpf1 variant fused to MS2 coat protein, endoribonuclease Csy4, or lambda N can be used to recruit a long non-coding RNA (lncRNA) such as XIST or HOTAIR; see, e.g., Keryer-Bibens et al., Biol. Cell 100:125-138 (2008), that is linked to the Csy4, MS2 or lambda N binding sequence. Alternatively, the Csy4, MS2 or lambda N protein binding sequence can be linked to another protein, e.g., as described in Keryer-Bibens et al., supra, and the protein can be targeted to the dCpf1 variant binding site using the methods and compositions described herein. In some embodiments, the Csy4 is catalytically inactive. In some embodiments, the Cpf1 variant, preferably a dCpf1 variant, is fused to FokI as described in U.S. Pat. No. 8,993,233; US 20140186958; U.S. Pat. No. 9,023,649; WO/2014/099744; WO 2014/089290; WO2014/144592; WO144288; WO2014/204578; WO2014/152432; WO2115/099850; U.S. Pat. No. 8,697,359; US2010/0076057; US2011/0189776; US2011/0223638; US2013/0130248; WO/2008/108989; WO/2010/054108; WO/2012/164565; WO/2013/098244; WO/2013/176772; US20150050699; US 20150071899 and WO 2014/204578.

In some embodiments, the fusion proteins include a linker between the Cpf1 variant and the heterologous functional domains. Linkers that can be used in these fusion proteins (or between fusion proteins in a concatenated structure) can include any sequence that does not interfere with the function of the fusion proteins. In preferred embodiments, the linkers are short, e.g., 2-20 amino acids, and are typically flexible (i.e., comprising amino acids with a high degree of freedom such as glycine, alanine, and serine). In some embodiments, the linker comprises one or more units consisting of GGGS (SEQ ID NO:3) or GGGGS (SEQ ID NO:4), e.g., two, three, four, or more repeats of the GGGS (SEQ ID NO:5) or GGGGS (SEQ ID NO:6) unit. Other linker sequences can also be used.

In some embodiments, the variant protein includes a cell-penetrating peptide sequence that facilitates delivery to the intracellular space, e.g., HIV-derived TAT peptide, penetratins, transportans, or hCT derived cell-penetrating peptides, see, e.g., Caron et al., (2001) Mol Ther. 3(3):310-8; Langel, Cell-Penetrating Peptides: Processes and Applications (CRC Press, Boca Raton Fla. 2002); El-Andaloussi et al., (2005) Curr Pharm Des. 11(28):3597-611; and Deshayes et al., (2005) Cell Mol Life Sci. 62(16):1839-49.

Cell penetrating peptides (CPPs) are short peptides that facilitate the movement of a wide range of biomolecules across the cell membrane into the cytoplasm or other organelles, e.g. the mitochondria and the nucleus. Examples of molecules that can be delivered by CPPs include therapeutic drugs, plasmid DNA, oligonucleotides, siRNA, peptide-nucleic acid (PNA), proteins, peptides, nanoparticles, and liposomes. CPPs are generally 30 amino acids or less, are derived from naturally or non-naturally occurring protein or chimeric sequences, and contain either a high relative abundance of positively charged amino acids, e.g. lysine or arginine, or an alternating pattern of polar and non-polar amino acids. CPPs that are commonly used in the art include Tat (Frankel et al., (1988) Cell. 55:1189-1193, Vives et al., (1997) J. Biol. Chem. 272:16010-16017), penetratin (Derossi et al., (1994) J. Biol. Chem. 269:10444-10450), polyarginine peptide sequences (Wender et al., (2000) Proc. Natl. Acad. Sci. USA 97:13003-13008, Futaki et al., (2001) J. Biol. Chem. 276:5836-5840), and transportan (Pooga et al., (1998) Nat. Biotechnol. 16:857-861).

CPPs can be linked with their cargo through covalent or non-covalent strategies. Methods for covalently joining a CPP and its cargo are known in the art, e.g. chemical cross-linking (Stetsenko et al., (2000) J. Org. Chem. 65:4900-4909, Gait et al. (2003) Cell. Mol. Life. Sci. 60:844-853) or cloning a fusion protein (Nagahara et al., (1998) Nat. Med. 4:1449-1453). Non-covalent coupling between the cargo and short amphipathic CPPs comprising polar and non-polar domains is established through electrostatic and hydrophobic interactions.

CPPs have been utilized in the art to deliver potentially therapeutic biomolecules into cells. Examples include cyclosporine linked to polyarginine for immunosuppression (Rothbard et al., (2000) Nature Medicine 6(11):1253-1257), siRNA against cyclin B1 linked to a CPP called MPG for inhibiting tumorigenesis (Crombez et al., (2007) Biochem Soc. Trans. 35:44-46), tumor suppressor p53 peptides linked to CPPs to reduce cancer cell growth (Takenobu et al., (2002) Mol. Cancer Ther. 1(12):1043-1049, Snyder et al., (2004) PLoS Biol. 2:E36), and dominant negative forms of Ras or phosphoinositol 3 kinase (PI3K) fused to Tat to treat asthma (Myou et al., (2003) J. Immunol. 171:4399-4405).

CPPs have been utilized in the art to transport contrast agents into cells for imaging and biosensing applications. For example, green fluorescent protein (GFP) attached to Tat has been used to label cancer cells (Shokolenko et al., (2005) DNA Repair 4(4):511-518). Tat conjugated to quantum dots have been used to successfully cross the blood-brain barrier for visualization of the rat brain (Santra et al., (2005) Chem. Commun. 3144-3146). CPPs have also been combined with magnetic resonance imaging techniques for cell imaging (Liu et al., (2006) Biochem. and Biophys. Res. Comm. 347(1):133-140). See also Ramsey and Flynn, Pharmacol Ther. 2015 Jul. 22. pii: S0163-7258(15)00141-2.

Alternatively or in addition, the variant proteins can include a nuclear localization sequence, e.g., SV40 large T antigen NLS (PKKKRRV (SEQ ID NO:7)) and nucleoplasmin NLS (KRPAATKKAGQAKKKK (SEQ ID NO:8)). Other NLSs are known in the art; see, e.g., Cokol et al., EMBO Rep. 2000 Nov. 15; 1(5): 411-415; Freitas and Cunha, Curr Genomics. 2009 December; 10(8): 550-557.

In some embodiments, the variants include a moiety that has a high affinity for a ligand, for example GST, FLAG or hexahistidine sequences. Such affinity tags can facilitate the purification of recombinant variant proteins.

For methods in which the variant proteins are delivered to cells, the proteins can be produced using any method known in the art, e.g., by in vitro translation, or expression in a suitable host cell from nucleic acid encoding the variant protein; a number of methods are known in the art for producing proteins. For example, the proteins can be produced in and purified from yeast, E. coli, insect cell lines, plants, transgenic animals, or cultured mammalian cells; see, e.g., Palomares et al., “Production of Recombinant Proteins: Challenges and Solutions,” Methods Mol Biol. 2004; 267:15-52. In addition, the variant proteins can be linked to a moiety that facilitates transfer into a cell, e.g., a lipid nanoparticle, optionally with a linker that is cleaved once the protein is inside the cell. See, e.g., LaFountaine et al., Int J Pharm. 2015 Aug. 13; 494(1):180-194.

Expression Systems

To use the Cpf1 variants described herein, it may be desirable to express them from a nucleic acid that encodes them. This can be performed in a variety of ways. For example, the nucleic acid encoding the Cpf1 variant can be cloned into an intermediate vector for transformation into prokaryotic or eukaryotic cells for replication and/or expression. Intermediate vectors are typically prokaryote vectors, e.g., plasmids, or shuttle vectors, or insect vectors, for storage or manipulation of the nucleic acid encoding the Cpf1 variant for production of the Cpf1 variant. The nucleic acid encoding the Cpf1 variant can also be cloned into an expression vector, for administration to a plant cell, animal cell, preferably a mammalian cell or a human cell, fungal cell, bacterial cell, or protozoan cell.

To obtain expression, a sequence encoding a Cpf1 variant is typically subcloned into an expression vector that contains a promoter to direct transcription. Suitable bacterial and eukaryotic promoters are well known in the art and described, e.g., in Sambrook et al., Molecular Cloning, A Laboratory Manual (3d ed. 2001); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., eds., 2010). Bacterial expression systems for expressing the engineered protein are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al., 1983, Gene 22:229-235). Kits for such expression systems are commercially available. Eukaryotic expression systems for mammalian cells, yeast, and insect cells are well known in the art and are also commercially available.

The promoter used to direct expression of a nucleic acid depends on the particular application. For example, a strong constitutive promoter is typically used for expression and purification of fusion proteins. In contrast, when the Cpf1 variant is to be administered in vivo for gene regulation, either a constitutive or an inducible promoter can be used, depending on the particular use of the Cpf1 variant. In addition, a preferred promoter for administration of the Cpf1 variant can be a weak promoter, such as HSV TK or a promoter having similar activity. The promoter can also include elements that are responsive to transactivation, e.g., hypoxia response elements, Gal4 response elements, lac repressor response element, and small molecule control systems such as tetracycline-regulated systems and the RU-486 system (see, e.g., Gossen & Bujard, 1992, Proc. Natl. Acad. Sci. USA, 89:5547; Oligino et al., 1998, Gene Ther., 5:491-496; Wang et al., 1997, Gene Ther., 4:432-441; Neering et al., 1996, Blood, 88:1147-55; and Rendahl et al., 1998, Nat. Biotechnol., 16:757-761).

In addition to the promoter, the expression vector typically contains a transcription unit or expression cassette that contains all the additional elements required for the expression of the nucleic acid in host cells, either prokaryotic or eukaryotic. A typical expression cassette thus contains a promoter operably linked, e.g., to the nucleic acid sequence encoding the Cpf1 variant, and any signals required, e.g., for efficient polyadenylation of the transcript, transcriptional termination, ribosome binding sites, or translation termination. Additional elements of the cassette may include, e.g., enhancers, and heterologous spliced intronic signals.

The particular expression vector used to transport the genetic information into the cell is selected with regard to the intended use of the Cpf1 variant, e.g., expression in plants, animals, bacteria, fungus, protozoa, etc. Standard bacterial expression vectors include plasmids such as pBR322 based plasmids, pSKF, pET23D, and commercially available tag-fusion expression systems such as GST and LacZ.

Expression vectors containing regulatory elements from eukaryotic viruses are often used in eukaryotic expression vectors, e.g., SV40 vectors, papilloma virus vectors, and vectors derived from Epstein-Barr virus. Other exemplary eukaryotic vectors include pMSG, pAV009/A+, pMTO10/A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV40 early promoter, SV40 late promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.

The vectors for expressing the Cpf1 variants can include RNA Pol III promoters to drive expression of the guide RNAs, e.g., the H1, U6 or 7SK promoters. These human promoters allow for expression of Cpf1 variants in mammalian cells following plasmid transfection.

Some expression systems have markers for selection of stably transfected cell lines such as thymidine kinase, hygromycin B phosphotransferase, and dihydrofolate reductase. High yield expression systems are also suitable, such as using a baculovirus vector in insect cells, with the gRNA encoding sequence under the direction of the polyhedrin promoter or other strong baculovirus promoters.

The elements that are typically included in expression vectors also include a replicon that functions in E. coli, a gene encoding antibiotic resistance to permit selection of bacteria that harbor recombinant plasmids, and unique restriction sites in nonessential regions of the plasmid to allow insertion of recombinant sequences.

Standard transfection methods are used to produce bacterial, mammalian, yeast or insect cell lines that express large quantities of protein, which are then purified using standard techniques (see, e.g., Colley et al., 1989, J. Biol. Chem., 264:17619-22; Guide to Protein Purification, in Methods in Enzymology, vol. 182 (Deutscher, ed., 1990)). Transformation of eukaryotic and prokaryotic cells are performed according to standard techniques (see, e.g., Morrison, 1977, J. Bacteriol. 132:349-351; Clark-Curtiss & Curtiss, Methods in Enzymology 101:347-362 (Wu et al., eds, 1983).

Any of the known procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, polybrene, protoplast fusion, electroporation, nucleofection, liposomes, microinjection, naked DNA, plasmid vectors, viral vectors, both episomal and integrative, and any of the other well-known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Sambrook et al., supra). It is only necessary that the particular genetic engineering procedure used be capable of successfully introducing at least one gene into the host cell capable of expressing the Cpf1 variant.

The present invention also includes the vectors and cells comprising the vectors.

Examples

The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.

Sequences

The following constructs were used in the Examples below.

Nucleotide sequence of pCAG-humanAsCpfl-NLS-3xHA Human codon optimized AsCpf1 in normal font (NTs 1-3921), NLS in lower case (aaaaggccggcggccacgaaaaaggccggccaggcaaaaaagaaaaag, SEQ ID NO: 3), 3xHA tag (TACCCATACGATGTTCCAGATTACGCTTATCCCTACGACGTGCCTGATTATGCATACCCATAT GATGTCCCCGACTATGCC, SEQ ID NO: 4) in bold ATGACACAGTTCGAGGGCTTTACCAACCTGTATCAGGTGAGCAAGACACTGCGGTTTGAGCTGATCCCACAG GGCAAGACCCTGAAGCACATCCAGGAGCAGGGCTTCATCGAGGAGGACAAGGCCCGCAATGATCACTACAAGGAGCT GAAGCCCATCATCGATCGGATCTACAAGACCTATGCCGACCAGTGCCTGCAGCTGGTGCAGCTGGATTGGGAGAACCT GAGCGCCGCCATCGACTCCTATAGAAAGGAGAAAACCGAGGAGACAAGGAACGCCCTGATCGAGGAGCAGGCCACAT ATCGCAATGCCATCCACGACTACTTCATCGGCCGGACAGACAACCTGACCGATGCCATCAATAAGAGACACGCCGAGA TCTACAAGGGCCTGTTCAAGGCCGAGCTGTTTAATGGCAAGGTGCTGAAGCAGCTGGGCACCGTGACCACAACCGAG CACGAGAACGCCCTGCTGCGGAGCTTCGACAAGTTTACAACCTACTTCTCCGGCTTTTATGAGAACAGGAAGAACGTG TTCAGCGCCGAGGATATCAGCACAGCCATCCCACACCGCATCGTGCAGGACAACTTCCCCAAGTTTAAGGAGAATTGT CACATCTTCACACGCCTGATCACCGCCGTGCCCAGCCTGCGGGAGCACTTTGAGAACGTGAAGAAGGCCATCGGCAT CTTCGTGAGCACCTCCATCGAGGAGGTGTTTTCCTTCCCTTTTTATAACCAGCTGCTGACACAGACCCAGATCGACCTG TATAACCAGCTGCTGGGAGGAATCTCTCGGGAGGCAGGCACCGAGAAGATCAAGGGCCTGAACGAGGTGCTGAATCT GGCCATCCAGAAGAATGATGAGACAGCCCACATCATCGCCTCCCTGCCACACAGATTCATCCCCCTGTTTAAGCAGAT CCTGTCCGATAGGAACACCCTGTCTTTCATCCTGGAGGAGTTTAAGAGCGACGAGGAAGTGATCCAGTCCTTCTGCAA GTACAAGACACTGCTGAGAAACGAGAACGTGCTGGAGACAGCCGAGGCCCTGTTTAACGAGCTGAACAGCATCGACC TGACACACATCTTCATCAGCCACAAGAAGCTGGAGACAATCAGCAGCGCCCTGTGCGACCACTGGGATACACTGAGGA ATGCCCTGTATGAGCGGAGAATCTCCGAGCTGACAGGCAAGATCACCAAGTCTGCCAAGGAGAAGGTGCAGCGCAGC CTGAAGCACGAGGATATCAACCTGCAGGAGATCATCTCTGCCGCAGGCAAGGAGCTGAGCGAGGCCTTCAAGCAGAA AACCAGCGAGATCCTGTCCCACGCACACGCCGCCCTGGATCAGCCACTGCCTACAACCCTGAAGAAGCAGGAGGAGA AGGAGATCCTGAAGTCTCAGCTGGACAGCCTGCTGGGCCTGTACCACCTGCTGGACTGGTTTGCCGTGGATGAGTCC AACGAGGTGGACCCCGAGTTCTCTGCCCGGCTGACCGGCATCAAGCTGGAGATGGAGCCTTCTCTGAGCTTCTACAA CAAGGCCAGAAATTATGCCACCAAGAAGCCCTACTCCGTGGAGAAGTTCAAGCTGAACTTTCAGATGCCTACACTGGC CTCTGGCTGGGACGTGAATAAGGAGAAGAACAATGGCGCCATCCTGTTTGTGAAGAACGGCCTGTACTATCTGGGCAT CATGCCAAAGCAGAAGGGCAGGTATAAGGCCCTGAGCTTCGAGCCCACAGAGAAAACCAGCGAGGGCTTTGATAAGA TGTACTATGACTACTTCCCTGATGCCGCCAAGATGATCCCAAAGTGCAGCACCCAGCTGAAGGCCGTGACAGCCCACT TTCAGACCCACACAACCCCCATCCTGCTGTCCAACAATTTCATCGAGCCTCTGGAGATCACAAAGGAGATCTACGACCT GAACAATCCTGAGAAGGAGCCAAAGAAGTTTCAGACAGCCTACGCCAAGAAAACCGGCGACCAGAAGGGCTACAGAG AGGCCCTGTGCAAGTGGATCGACTTCACAAGGGATTTTCTGTCCAAGTATACCAAGACAACCTCTATCGATCTGTCTAG CCTGCGGCCATCCTCTCAGTATAAGGACCTGGGCGAGTACTATGCCGAGCTGAATCCCCTGCTGTACCACATCAGCTT CCAGAGAATCGCCGAGAAGGAGATCATGGATGCCGTGGAGACAGGCAAGCTGTACCTGTTCCAGATCTATAACAAGGA CTTTGCCAAGGGCCACCACGGCAAGCCTAATCTGCACACACTGTATTGGACCGGCCTGTTTTCTCCAGAGAACCTGGC CAAGACAAGCATCAAGCTGAATGGCCAGGCCGAGCTGTTCTACCGCCCTAAGTCCAGGATGAAGAGGATGGCACACC GGCTGGGAGAGAAGATGCTGAACAAGAAGCTGAAGGATCAGAAAACCCCAATCCCCGACACCCTGTACCAGGAGCTG TACGACTATGTGAATCACAGACTGTCCCACGACCTGTCTGATGAGGCCAGGGCCCTGCTGCCCAACGTGATCACCAAG GAGGTGTCTCACGAGATCATCAAGGATAGGCGCTTTACCAGCGACAAGTTCTTTTTCCACGTGCCTATCACACTGAACT ATCAGGCCGCCAATTCCCCATCTAAGTTCAACCAGAGGGTGAATGCCTACCTGAAGGAGCACCCCGAGACACCTATCA TCGGCATCGATCGGGGCGAGAGAAACCTGATCTATATCACAGTGATCGACTCCACCGGCAAGATCCTGGAGCAGCGG AGCCTGAACACCATCCAGCAGTTTGATTACCAGAAGAAGCTGGACAACAGGGAGAAGGAGAGGGTGGCAGCAAGGCA GGCCTGGTCTGTGGTGGGCACAATCAAGGATCTGAAGCAGGGCTATCTGAGCCAGGTCATCCACGAGATCGTGGACC TGATGATCCACTACCAGGCCGTGGTGGTGCTGGAGAACCTGAATTTCGGCTTTAAGAGCAAGAGGACCGGCATCGCC GAGAAGGCCGTGTACCAGCAGTTCGAGAAGATGCTGATCGATAAGCTGAATTGCCTGGTGCTGAAGGACTATCCAGCA GAGAAAGTGGGAGGCGTGCTGAACCCATACCAGCTGACAGACCAGTTCACCTCCTTTGCCAAGATGGGCACCCAGTCT GGCTTCCTGTTTTACGTGCCTGCCCCATATACATCTAAGATCGATCCCCTGACCGGCTTCGTGGACCCCTTCGTGTGGA AAACCATCAAGAATCACGAGAGCCGCAAGCACTTCCTGGAGGGCTTCGACTTTCTGCACTACGACGTGAAAACCGGCG ACTTCATCCTGCACTTTAAGATGAACAGAAATCTGTCCTTCCAGAGGGGCCTGCCCGGCTTTATGCCTGCATGGGATAT CGTGTTCGAGAAGAACGAGACACAGTTTGACGCCAAGGGCACCCCTTTCATCGCCGGCAAGAGAATCGTGCCAGTGAT CGAGAATCACAGATTCACCGGCAGATACCGGGACCTGTATCCTGCCAACGAGCTGATCGCCCTGCTGGAGGAGAAGG GCATCGTGTTCAGGGATGGCTCCAACATCCTGCCAAAGCTGCTGGAGAATGACGATTCTCACGCCATCGACACCATGG TGGCCCTGATCCGCAGCGTGCTGCAGATGCGGAACTCCAATGCCGCCACAGGCGAGGACTATATCAACAGCCCCGTG CGCGATCTGAATGGCGTGTGCTTCGACTCCCGGTTTCAGAACCCAGAGTGGCCCATGGACGCCGATGCCAATGGCGC CTACCACATCGCCCTGAAGGGCCAGCTGCTGCTGAATCACCTGAAGGAGAGCAAGGATCTGAAGCTGCAGAACGGCA TCTCCAATCAGGACTGGCTGGCCTACATCCAGGAGCTGCGCAACaaaaggccggcggccacgaaaaaggccggccaggcaaaaaagaa aaagGGATCCTACCCATACGATGTTCCAGATTACGCTTATCCCTACGACGTGCCTGATTATGCATACCCATATGATGTC CCCGACTATGCCTAA (SEQ ID NO: 5) Amino acid sequence of AsCpf1-NLS-3xHA AsCpf1 in normal font (AAs 1-1306), NLS (krpaatkkagqakkkkgs, SEQ ID NO: 6) in lower case, 3xHA tag (YPYDVPDYAYPYDVPDYAYPYDVPDYA, SEQ ID NO: 7) in bold MTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRIYKTYADQCLQLVQLDWENLS AAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDNLTDAINKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSF DKFTTYFSGFYENRKNVFSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSIEEVFSFPFYNQ LLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIASLPHRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKY KTLLRNENVLETAEALFNELNSIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHEDINLQE1 ISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLGLYHLLDWFAVDESNEVDPEFSARLTGIKLEM EPSLSFYNKARNYATKKPYSVEKFKLNFQMPTLASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEG FDKMYYDYFPDAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQTAYAKKTGDQKGYREAL CKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPLLYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKP NLHTLYVVTGLFSPENLAKTSIKLNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHDLSD EARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQAANSPSKFNQRVNAYLKEHPETPIIGIDRGERNLIYITVIDSTGKI LE QRSLNTIQQFDYQKKLDNREKERVAARQAWSVVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAV YQQFEKMLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLTGFVDPFVWKTIKNHES RKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAWDIVFEKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDL YPANELIALLEEKGIVFIRDGSNILPKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRPQNPEWP MDADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRNkrpaatkkagqakkkkgsYPYDVPDYAYPYDVPDYAYP YDVPDYA (SEQ ID NO: 8) Nucleotide sequence of SQT1665 pCAG-humanLbCpf1-NLS-3xHA Human codon optimized LbCpf1 in normal font, nts 1-3684), NLS (aaaaggccggcggccacgaaaaaggccggccaggcaaaaaagaaaaag, SEQ ID NO: 3) in lower case, 3xHA tag (TACCCATACGATGTTCCAGATTACGCTTATCCCTACGACGTGCCTGATTATGCATACCCATAT GATGTCCCCGACTATGCC, SEQ ID NO: 4) in BOLD ATGAGCAAGCTGGAGAAGTTTACAAACTGCTACTCCCTGTCTAAGACCCTGAGGTTCAAGGCCATCCCTGTG GGCAAGACCCAGGAGAACATCGACAATAAGCGGCTGCTGGTGGAGGACGAGAAGAGAGCCGAGGATTATAAGGGCGT GAAGAAGCTGCTGGATCGCTACTATCTGTCTTTTATCAACGACGTGCTGCACAGCATCAAGCTGAAGAATCTGAACAAT TACATCAGCCTGTTCCGGAAGAAAACCAGAACCGAGAAGGAGAATAAGGAGCTGGAGAACCTGGAGATCAATCTGCGG AAGGAGATCGCCAAGGCCTTCAAGGGCAACGAGGGCTACAAGTCCCTGTTTAAGAAGGATATCATCGAGACAATCCTG CCAGAGTTCCTGGACGATAAGGACGAGATCGCCCTGGTGAACAGCTTCAATGGCTTTACCACAGCCTTCACCGGCTTC TTTGATAACAGAGAGAATATGTTTTCCGAGGAGGCCAAGAGCACATCCATCGCCTTCAGGTGTATCAACGAGAATCTGA CCCGCTACATCTCTAATATGGACATCTTCGAGAAGGTGGACGCCATCTTTGATAAGCACGAGGTGCAGGAGATCAAGG AGAAGATCCTGAACAGCGACTATGATGTGGAGGATTTCTTTGAGGGCGAGTTCTTTAACTTTGTGCTGACACAGGAGG GCATCGACGTGTATAACGCCATCATCGGCGGCTTCGTGACCGAGAGCGGCGAGAAGATCAAGGGCCTGAACGAGTAC ATCAACCTGTATAATCAGAAAACCAAGCAGAAGCTGCCTAAGTTTAAGCCACTGTATAAGCAGGTGCTGAGCGATCGGG AGTCTCTGAGCTTCTACGGCGAGGGCTATACATCCGATGAGGAGGTGCTGGAGGTGTTTAGAAACACCCTGAACAAGA ACAGCGAGATCTTCAGCTCCATCAAGAAGCTGGAGAAGCTGTTCAAGAATTTTGACGAGTACTCTAGCGCCGGCATCTT TGTGAAGAACGGCCCCGCCATCAGCACAATCTCCAAGGATATCTTCGGCGAGTGGAACGTGATCCGGGACAAGTGGA ATGCCGAGTATGACGATATCCACCTGAAGAAGAAGGCCGTGGTGACCGAGAAGTACGAGGACGATCGGAGAAAGTCC TTCAAGAAGATCGGCTCCTTTTCTCTGGAGCAGCTGCAGGAGTACGCCGACGCCGATCTGTCTGTGGTGGAGAAGCTG AAGGAGATCATCATCCAGAAGGTGGATGAGATCTACAAGGTGTATGGCTCCTCTGAGAAGCTGTTCGACGCCGATTTT GTGCTGGAGAAGAGCCTGAAGAAGAACGACGCCGTGGTGGCCATCATGAAGGACCTGCTGGATTCTGTGAAGAGCTT CGAGAATTACATCAAGGCCTTCTTTGGCGAGGGCAAGGAGACAAACAGGGACGAGTCCTTCTATGGCGATTTTGTGCT GGCCTACGACATCCTGCTGAAGGTGGACCACATCTACGATGCCATCCGCAATTATGTGACCCAGAAGCCCTACTCTAA GGATAAGTTCAAGCTGTATTTTCAGAACCCTCAGTTCATGGGCGGCTGGGACAAGGATAAGGAGACAGACTATCGGGC CACCATCCTGAGATACGGCTCCAAGTACTATCTGGCCATCATGGATAAGAAGTACGCCAAGTGCCTGCAGAAGATCGA CAAGGACGATGTGAACGGCAATTACGAGAAGATCAACTATAAGCTGCTGCCCGGCCCTAATAAGATGCTGCCAAAGGT GTTCTTTTCTAAGAAGTGGATGGCCTACTATAACCCCAGCGAGGACATCCAGAAGATCTACAAGAATGGCACATTCAAG AAGGGCGATATGTTTAACCTGAATGACTGTCACAAGCTGATCGACTTCTTTAAGGATAGCATCTCCCGGTATCCAAAGT GGTCCAATGCCTACGATTTCAACTTTTCTGAGACAGAGAAGTATAAGGACATCGCCGGCTTTTACAGAGAGGTGGAGG AGCAGGGCTATAAGGTGAGCTTCGAGTCTGCCAGCAAGAAGGAGGTGGATAAGCTGGTGGAGGAGGGCAAGCTGTAT ATGTTCCAGATCTATAACAAGGACTTTTCCGATAAGTCTCACGGCACACCCAATCTGCACACCATGTACTTCAAGCTGCT GTTTGACGAGAACAATCACGGACAGATCAGGCTGAGCGGAGGAGCAGAGCTGTTCATGAGGCGCGCCTCCCTGAAGA AGGAGGAGCTGGTGGTGCACCCAGCCAACTCCCCTATCGCCAACAAGAATCCAGATAATCCCAAGAAAACCACAACCC TGTCCTACGACGTGTATAAGGATAAGAGGTTTTCTGAGGACCAGTACGAGCTGCACATCCCAATCGCCATCAATAAGTG CCCCAAGAACATCTTCAAGATCAATACAGAGGTGCGCGTGCTGCTGAAGCACGACGATAACCCCTATGTGATCGGCAT CGATAGGGGCGAGCGCAATCTGCTGTATATCGTGGTGGTGGACGGCAAGGGCAACATCGTGGAGCAGTATTCCCTGA ACGAGATCATCAACAACTTCAACGGCATCAGGATCAAGACAGATTACCACTCTCTGCTGGACAAGAAGGAGAAGGAGA GGTTCGAGGCCCGCCAGAACTGGACCTCCATCGAGAATATCAAGGAGCTGAAGGCCGGCTATATCTCTCAGGTGGTG CACAAGATCTGCGAGCTGGTGGAGAAGTACGATGCCGTGATCGCCCTGGAGGACCTGAACTCTGGCTTTAAGAATAGC CGCGTGAAGGTGGAGAAGCAGGTGTATCAGAAGTTCGAGAAGATGCTGATCGATAAGCTGAACTACATGGTGGACAAG AAGTCTAATCCTTGTGCAACAGGCGGCGCCCTGAAGGGCTATCAGATCACCAATAAGTTCGAGAGCTTTAAGTCCATGT CTACCCAGAACGGCTTCATCTTTTACATCCCTGCCTGGCTGACATCCAAGATCGATCCATCTACCGGCTTTGTGAACCT GCTGAAAACCAAGTATACCAGCATCGCCGATTCCAAGAAGTTCATCAGCTCCTTTGACAGGATCATGTACGTGCCCGAG GAGGATCTGTTCGAGTTTGCCCTGGACTATAAGAACTTCTCTCGCACAGACGCCGATTACATCAAGAAGTGGAAGCTGT ACTCCTACGGCAACCGGATCAGAATCTTCCGGAATCCTAAGAAGAACAACGTGTTCGACTGGGAGGAGGTGTGCCTGA CCAGCGCCTATAAGGAGCTGTTCAACAAGTACGGCATCAATTATCAGCAGGGCGATATCAGAGCCCTGCTGTGCGAGC AGTCCGACAAGGCCTTCTACTCTAGCTTTATGGCCCTGATGAGCCTGATGCTGCAGATGCGGAACAGCATCACAGGCC GCACCGACGTGGATTTTCTGATCAGCCCTGTGAAGAACTCCGACGGCATCTTCTACGATAGCCGGAACTATGAGGCCC AGGAGAATGCCATCCTGCCAAAGAACGCCGACGCCAATGGCGCCTATAACATCGCCAGAAAGGTGCTGTGGGCCATC GGCCAGTTCAAGAAGGCCGAGGACGAGAAGCTGGATAAGGTGAAGATCGCCATCTCTAACAAGGAGTGGCTGGAGTA CGCCCAGACCAGCGTGAAGCACaaaaggccggeggccacgaaaaaggccggccaggcaaaaaagaaaaagGGATCCTACCCATACGAT GTTCCAGATTACGCTTATCCCTACGACGTGCCTGATTATGCATACCCATATGATGTCCCCGACTATGCCTAA (SEQ ID NO: 9) Amino acid sequence of LbCpf1-NLS-3xHA LbCpf1 in normal text (AAs 1-1228), NLS (krpaatkkagqakkkkgs, SEQ ID NO: 6) in lower case, 3xHA tag (YPYDVPDYAYPYDVPDYAYPYDVPDYA, SEQ ID NO: 7) in bold MSKLEKFTNCYSLSKTLRFKAIPVGKTQENIDNKRLLVEDEKRAEDYKGVKKLLDRYYLSFINDVLHSIKLKNLNNYI SLFRKKTRTEKENKELENLEI NLRKEIAKAFKGNEGYKSLFKKDIIETILPEFLDDKDEIALVNSFNGFTTAFTGFFDNRENMFSE EAKSTSIAFRCINENLTRYISNMDIFEKVDAIFDKHEVQEIKEKILNSDYDVEDFFEGEFFNFVLTQEGIDVYNAIIGGFVTESGE KIKGLNEYINLYNQKTKQKLPKFKPLYKQVLSDRESLSFYGEGYTSDEEVLEVFRNTLNKNSEIFSSIKKLEKLFKNFDEYSSA GIFVKNGPAISTISKDIFGEWNVIRDKWNAEYDDIHLKKKAVVTEKYEDDRRKSFKKIGSFSLEQLQEYADADLSVVEKLKEIIIQ KVDEIYKVYGSSEKLFDADFVLEKSLKKNDAVVAIMKDLLDSVKSFENYIKAFFGEGKETNRDESFYGDFVLAYDILLKVDHIY DAIRNYVTQKPYSKDKFKLYFQNPQFMGGWDKDKETDYRATILRYGSKYYLAIMDKKYAKCLQKIDKDDVNGNYEKINYKLL PGPNKMLPKVFFSKKWMAYYNPSEDIQKIYKNGTFKKGDMFNLNDCHKLIDFFKDSISRYPKWSNAYDFNFSETEKYKDIAG FYREVEEQGYKVSFESASKKEVDKLVEEGKLYMFQIYNKDFSDKSHGTPNLHTMYFKLLFDENNHGQIRLSGGAELFMRRA SLKKEELVVHPANSPIANKNPDNPKKTTTLSYDVYKDKRFSEDQYELHIPIAINKCPKNIFKINTEVRVLLKHDDNPYVIGIDRGE RNLLYIVVVDGKGNIVEQYSLNEIINNFNGIRIKTDYHSLLDKKEKERFEARQNVVTSIENIKELKAGYISQVVHKICELVEKYDAVI ALEDLNSGFKNSRVKVEKQVYQKFEKMLIDKLNYMVDKKSNPCATGGALKGYQITNKFESFKSMSTQNGFIFYIPAWLTSKID PSTGFVNLLKTKYTSIADSKKFISSFDRIMYVPEEDLFEFALDYKNFSRTDADYIKKWKLYSYGNRIRIFRNPKKNNVFDWEEV CLTSAYKELFNKYGINYQQGDIRALLCEQSDKAFYSSFMALMSLMLQMRNSITGRTDVDFLISPVKNSDGIFYDSRNYEAQEN AILPKNADANGAYNIARKVLWAIGQFKKAEDEKLDKVKIAISNKEWLEYAQTSVKHkrpaatkkagqakkkkgsYPYDVPDYAYPYD VPDYAYPYDVPDYA (SEQ ID NO: 10) Cpf1 crRNAs Spacer length Sequence with Cpf1 PAM at 5′ end Name (nt) (TTTC/TTTA/TTTG) SEQ ID NO DNMT1 DNMT1 site 1 23 TTTCCCTCACTCCTGCTCGGTGAATTT 11. DNMT1 site 1 mm 1&2 23 TTTCggTCACTCCTGCTCGGTGAATTT 12. DNMT1 site 1 mm 3&4 23 TTTCCCagACTCCTGCTCGGTGAATTT 13. DNMT1 site 1 mm 5&6 23 TTTCCCTCtgTCCTGCTCGGTGAATTT 14. DNMT1 site 1 mm 7&8 23 TTTCCCTCACagCTGCTCGGTGAATTT 15. DNMT1 site 1 mm 9&10 23 TTTCCCTCACTCgaGCTCGGTGAATTT 16. DNMT1 site 1 mm 11&12 23 TTTCCCTCACTCCTcgTCGGTGAATTT 17. DNMT1 site 1 mm 13&14 23 TTTCCCTCACTCCTGCagGGTGAATTT 18. DNMT1 site 1 mm 15&16 23 TTTCCCTCACTCCTGCTCccTGAATTT 19. DNMT1 site 1 mm 17&18 23 TTTCCCTCACTCCTGCTCGGacAATTT 20. DNMT1 site 1 mm 19&20 23 TTTCCCTCACTCCTGCTCGGTGttTTT 21. DNMT1 site 1 mm 21&22 23 TTTCCCTCACTCCTGCTCGGTGAAaaT 22. DNMT1 site 1 mm 22&23 23 TTTCCCTCACTCCTGCTCGGTGAATaa 23. DNMT1 site 1 mm 1 23 TTTCgCTCACTCCTGCTCGGTGAATTT 24. DNMT1 site 1 mm 2 23 TTTCCgTCACTCCTGCTCGGTGAATTT 25. DNMT1 site 1 mm 3 23 TTTCCCaCACTCCTGCTCGGTGAATTT 26. DNMT1 site 1 mm 4 23 TTTCCCTgACTCCTGCTCGGTGAATTT 27. DNMT1 site 1 mm 5 23 TTTCCCTCtCTCCTGCTCGGTGAATTT 28. DNMT1 site 1 mm 6 23 TTTCCCTCAgTCCTGCTCGGTGAATTT 29. DNMT1 site 1 mm 7 23 TTTCCCTCACaCCTGCTCGGTGAATTT 30. DNMT1 site 1 mm 8 23 TTTCCCTCACTgCTGCTCGGTGAATTT 31. DNMT1 site 1 mm 9 23 TTTCCCTCACTCgTGCTCGGTGAATTT 32. DNMT1 site 1 mm 10 23 TTTCCCTCACTCCaGCTCGGTGAATTT 33. DNMT1 site 1 mm 11 23 TTTCCCTCACTCCTcCTCGGTGAATTT 34. DNMT1 site 1 mm 12 23 TTTCCCTCACTCCTGgTCGGTGAATTT 35. DNMT1 site 1 mm 13 23 TTTCCCTCACTCCTGCaCGGTGAATTT 36. DNMT1 site 1 mm 14 23 TTTCCCTCACTCCTGCTgGGTGAATTT 37. DNMT1 site 1 mm 15 23 TTTCCCTCACTCCTGCTCcGTGAATTT 38. DNMT1 site 1 mm 16 23 TTTCCCTCACTCCTGCTCGcTGAATTT 39. DNMT1 site 1 mm 17 23 TTTCCCTCACTCCTGCTCGGaGAATTT 40. DNMT1 site 1 mm 18 23 TTTCCCTCACTCCTGCTCGGTcAATTT 41. DNMT1 site 1 mm 19 23 TTTCCCTCACTCCTGCTCGGTGtATTT 42. DNMT1 site 1 mm 20 23 TTTCCCTCACTCCTGCTCGGTGAtTTT 43. DNMT1 site 1 mm 21 23 TTTCCCTCACTCCTGCTCGGTGAAaTT 44. DNMT1 site 1 mm 22 23 TTTCCCTCACTCCTGCTCGGTGAATaT 45. DNMT1 site 1 mm 23 23 TTTCCCTCACTCCTGCTCGGTGAATTa 46. DNMT1 site 1 26 TTTCCCTCACTCCTGCTCGGTGAATTTGGC 47. DNMT1 site 1 25 TTTCCCTCACTCCTGCTCGGTGAATTTGG 48. DNMT1 site 1 24 TTTCCCTCACTCCTGCTCGGTGAATTTG 49. DNMT1 site 1 22 TTTCCCTCACTCCTGCTCGGTGAATT 50. DNMT1 site 1 21 TTTCCCTCACTCCTGCTCGGTGAAT 51. DNMT1 site 1 20 TTTCCCTCACTCCTGCTCGGTGAA 52. DNMT1 site 1 mm 1 20 TTTCgCTCACTCCTGCTCGGTGAA 53. DNMT1 site 1 mm 2 20 TTTCCgTCACTCCTGCTCGGTGAA 54. DNMT1 site 1 mm 3 20 TTTCCCaCACTCCTGCTCGGTGAA 55. DNMT1 site 1 mm 4 20 TTTCCCTgACTCCTGCTCGGTGAA 56. DNMT1 site 1 mm 5 20 TTTCCCTCtCTCCTGCTCGGTGAA 57. DNMT1 site 1 mm 6 20 TTTCCCTCAgTCCTGCTCGGTGAA 58. DNMT1 site 1 mm 7 20 TTTCCCTCACaCCTGCTCGGTGAA 59. DNMT1 site 1 mm 8 20 TTTCCCTCACTgCTGCTCGGTGAA 60. DNMT1 site 1 mm 9 20 TTTCCCTCACTCgTGCTCGGTGAA 61. DNMT1 site 1 mm 10 20 TTTCCCTCACTCCaGCTCGGTGAA 62. DNMT1 site 1 mm 11 20 TTTCCCTCACTCCTcCTCGGTGAA 63. DNMT1 site 1 mm 12 20 TTTCCCTCACTCCTGgTCGGTGAA 64. DNMT1 site 1 mm 13 20 TTTCCCTCACTCCTGCaCGGTGAA 65. DNMT1 site 1 mm 14 20 TTTCCCTCACTCCTGCTgGGTGAA 66. DNMT1 site 1 mm 15 20 TTTCCCTCACTCCTGCTCcGTGAA 67. DNMT1 site 1 mm 16 20 TTTCCCTCACTCCTGCTCGcTGAA 68. DNMT1 site 1 mm 17 20 TTTCCCTCACTCCTGCTCGGaGAA 69. DNMT1 site 1 mm 18 20 TTTCCCTCACTCCTGCTCGGTcAA 70. DNMT1 site 1 mm 19 20 TTTCCCTCACTCCTGCTCGGTGtA 71. DNMT1 site 1 mm 20 20 TTTCCCTCACTCCTGCTCGGTGAt 72. DNMT1 site 1 19 TTTCCCTCACTCCTGCTCGGTGA 73. DNMT1 site 1 18 TTTCCCTCACTCCTGCTCGGTG 74. DNMT1 site 1 17 TTTCCCTCACTCCTGCTCGGT 75. DNMT1 site 1 16 TTTCCCTCACTCCTGCTCGG 76. DNMT1 site 2 23 TTTGAGGAGTGTTCAGTCTCCGTGAAC 77. DNMT1 site 3 23 TTTCCTGATGGTCCATGTCTGTTACTC 78. DNMT1 site 3 mm 1&2 23 TTTCgaGATGGTCCATGTCTGTTACTC 79. DNMT1 site 3 mm 3&4 23 TTTCCTctTGGTCCATGTCTGTTACTC 80. DNMT1 site 3 mm 5&6 23 TTTCCTGAacGTCCATGTCTGTTACTC 81. DNMT1 site 3 mm 7&8 23 TTTCCTGATGcaCCATGTCTGTTACTC 82. DNMT1 site 3 mm 9&10 23 TTTCCTGATGGTggATGTCTGTTACTC 83. DNMT1 site 3 mm 11&12 23 TTTCCTGATGGTCCtaGTCTGTTACTC 84. DNMT1 site 3 mm 13&14 23 TTTCCTGATGGTCCATcaCTGTTACTC 85. DNMT1 site 3 mm 15&16 23 TTTCCTGATGGTCCATGTgaGTTACTC 86. DNMT1 site 3 mm 17&18 23 TTTCCTGATGGTCCATGTCTcaTACTC 87. DNMT1 site 3 mm 19&20 23 TTTCCTGATGGTCCATGTCTGTatCTC 88. DNMT1 site 3 mm 21&22 23 TTTCCTGATGGTCCATGTCTGTTAgaC 89. DNMT1 site 3 mm 22&23 23 TTTCCTGATGGTCCATGTCTGTTACag 90. DNMT1 site 3 mm 1 23 TTTCgTGATGGTCCATGTCTGTTACTC 91. DNMT1 site 3 mm 2 23 TTTCCaGATGGTCCATGTCTGTTACTC 92. DNMT1 site 3 mm 3 23 TTTCCTcATGGTCCATGTCTGTTACTC 93. DNMT1 site 3 mm 4 23 TTTCCTGtTGGTCCATGTCTGTTACTC 94. DNMT1 site 3 mm 5 23 TTTCCTGAaGGTCCATGTCTGTTACTC 95. DNMT1 site 3 mm 6 23 TTTCCTGATcGTCCATGTCTGTTACTC 96. DNMT1 site 3 mm 7 23 TTTCCTGATGcTCCATGTCTGTTACTC 97. DNMT1 site 3 mm 8 23 TTTCCTGATGGaCCATGTCTGTTACTC 98. DNMT1 site 3 mm 9 23 TTTCCTGATGGTgCATGTCTGTTACTC 99. DNMT1 site 3 mm 10 23 TTTCCTGATGGTCgATGTCTGTTACTC 100. DNMT1 site 3 mm 11 23 TTTCCTGATGGTCCtTGTCTGTTACTC 101. DNMT1 site 3 mm 12 23 TTTCCTGATGGTCCAaGTCTGTTACTC 102. DNMT1 site 3 mm 13 23 TTTCCTGATGGTCCATcTCTGTTACTC 103. DNMT1 site 3 mm 14 23 TTTCCTGATGGTCCATGaCTGTTACTC 104. DNMT1 site 3 mm 15 23 TTTCCTGATGGTCCATGTgTGTTACTC 105. DNMT1 site 3 mm 16 23 TTTCCTGATGGTCCATGTCaGTTACTC 106. DNMT1 site 3 mm 17 23 TTTCCTGATGGTCCATGTCTcTTACTC 107. DNMT1 site 3 mm 18 23 TTTCCTGATGGTCCATGTCTGaTACTC 108. DNMT1 site 3 mm 19 23 TTTCCTGATGGTCCATGTCTGTaACTC 109. DNMT1 site 3 mm 20 23 TTTCCTGATGGTCCATGTCTGTTtCTC 110. DNMT1 site 3 mm 21 23 TTTCCTGATGGTCCATGTCTGTTAgTC 111. DNMT1 site 3 mm 22 23 TTTCCTGATGGTCCATGTCTGTTACaC 112. DNMT1 site 3 mm 23 23 TTTCCTGATGGTCCATGTCTGTTACTg 113. DNMT1 site 3 26 TTTCCTGATGGTCCATGTCTGTTACTCGCC 114. DNMT1 site 3 25 TTTCCTGATGGTCCATGTCTGTTACTCGC 115. DNMT1 site 3 24 TTTCCTGATGGTCCATGTCTGTTACTCG 116. DNMT1 site 3 22 TTTCCTGATGGTCCATGTCTGTTACT 117. DNMT1 site 3 21 TTTCCTGATGGTCCATGTCTGTTAC 118. DNMT1 site 3 20 TTTCCTGATGGTCCATGTCTGTTA 119. DNMT1 site 3 mm 1 20 TTTCgTGATGGTCCATGTCTGTTA 120. DNMT1 site 3 mm 2 20 TTTCCaGATGGTCCATGTCTGTTA 121. DNMT1 site 3 mm 3 20 TTTCCTcATGGTCCATGTCTGTTA 122. DNMT1 site 3 mm 4 20 TTTCCTGtTGGTCCATGTCTGTTA 123. DNMT1 site 3 mm 5 20 TTTCCTGAaGGTCCATGTCTGTTA 124. DNMT1 site 3 mm 6 20 TTTCCTGATcGTCCATGTCTGTTA 125. DNMT1 site 3 mm 7 20 TTTCCTGATGcTCCATGTCTGTTA 126. DNMT1 site 3 mm 8 20 TTTCCTGATGGaCCATGTCTGTTA 127. DNMT1 site 3 mm 9 20 TTTCCTGATGGTgCATGTCTGTTA 128. DNMT1 site 3 mm 10 20 TTTCCTGATGGTCgATGTCTGTTA 129. DNMT1 site 3 mm 11 20 TTTCCTGATGGTCCtTGTCTGTTA 130. DNMT1 site 3 mm 12 20 TTTCCTGATGGTCCAaGTCTGTTA 131. DNMT1 site 3 mm 13 20 TTTCCTGATGGTCCATcTCTGTTA 132. DNMT1 site 3 mm 14 20 TTTCCTGATGGTCCATGaCTGTTA 133. DNMT1 site 3 mm 15 20 TTTCCTGATGGTCCATGTgTGTTA 134. DNMT1 site 3 mm 16 20 TTTCCTGATGGTCCATGTCaGTTA 135. DNMT1 site 3 mm 17 20 TTTCCTGATGGTCCATGTCTcTTA 136. DNMT1 site 3 mm 18 20 TTTCCTGATGGTCCATGTCTGaTA 137. DNMT1 site 3 mm 19 20 TTTCCTGATGGTCCATGTCTGTaA 138. DNMT1 site 3 mm 20 20 TTTCCTGATGGTCCATGTCTGTTt 139. DNMT1 site 3 19 TTTCCTGATGGTCCATGTCTGTT 140. DNMT1 site 3 18 TTTCCTGATGGTCCATGTCTGT 141. DNMT1 site 3 17 TTTCCTGATGGTCCATGTCTG 142. DNMT1 site 3 16 TTTCCTGATGGTCCATGTCT 143. DNMT1 site 4 23 TTTATTTCCCTTCAGCTAAAATAAAGG 144. DNMT1 site 5 23 TTTATTTTAGCTGAAGGGAAATAAAAG 145. DNMT1 site 6 23 TTTTATTTCCCTTCAGCTAAAATAAAG 146. DNMT1 site 7 23 TTTGGCTCAGCAGGCACCTGCCTCAGC 147. DNMT1 site 7 mm 1&2 23 TTTGcgTCAGCAGGCACCTGCCTCAGC 148. DNMT1 site 7 mm 3&4 23 TTTGGCagAGCAGGCACCTGCCTCAGC 149. DNMT1 site 7 mm 5&6 23 TTTGGCTCtcCAGGCACCTGCCTCAGC 150. DNMT1 site 7 mm 7&8 23 TTTGGCTCAGgtGGCACCTGCCTCAGC 151. DNMT1 site 7 mm 9&10 23 TTTGGCTCAGCAccCACCTGCCTCAGC 152. DNMT1 site 7 mm 11&12 23 TTTGGCTCAGCAGGgtCCTGCCTCAGC 153. DNMT1 site 7 mm 13&14 23 TTTGGCTCAGCAGGCAggTGCCTCAGC 154. DNMT1 site 7 mm 15&16 23 TTTGGCTCAGCAGGCACCacCCTCAGC 155. DNMT1 site 7 mm 17&18 23 TTTGGCTCAGCAGGCACCTGggTCAGC 156. DNMT1 site 7 mm 19&20 23 TTTGGCTCAGCAGGCACCTGCCagAGC 157. DNMT1 site 7 mm 21&22 23 TTTGGCTCAGCAGGCACCTGCCTCtcC 158. DNMT1 site 7 mm 22&23 23 TTTGGCTCAGCAGGCACCTGCCTCAcg 159. DNMT1 site 7 26 TTTGGCTCAGCAGGCACCTGCCTCAGCTGC 160. DNMT1 site 7 25 TTTGGCTCAGCAGGCACCTGCCTCAGCTG 161. DNMT1 site 7 24 TTTGGCTCAGCAGGCACCTGCCTCAGCT 162. DNMT1 site 7 22 TTTGGCTCAGCAGGCACCTGCCTCAG 163. DNMT1 site 7 21 TTTGGCTCAGCAGGCACCTGCCTCA 164. DNMT1 site 7 20 TTTGGCTCAGCAGGCACCTGCCTC 165. DNMT1 site 7 19 TTTGGCTCAGCAGGCACCTGCCT 166. DNMT1 site 7 18 TTTGGCTCAGCAGGCACCTGCC 167. DNMT1 site 7 17 TTTGGCTCAGCAGGCACCTGC 168. DNMT1 site 7 16 TTTGGCTCAGCAGGCACCTG 169. EMX1 EMX1 site 1 23 TTTCTCATCTGTGCCCCTCCCTCCCTG 170. EMX1 site 2 23 TTTGTCCTCCGGTTCTGGAACCACACC 171. EMX1 site 3 23 TTTGTGGTTGCCCACCCTAGTCATTGG 172. EMX1 site 4 23 TTTGTACTTTGTCCTCCGGTTCTGGAA 173. FANCF FANCF site 1 23 TTTGGGCGGGGTCCAGTTCCGGGATTA 174. FANCF site 2 23 TTTGGTCGGCATGGCCCCATTCGCACG 175. FANCF site 3 23 TTTTCCGAGCTTCTGGCGGTCTCAAGC 176. FANCF site 4 23 TTTCACCTTGGAGACGGCGACTCTCTG 177. RUNX1 RUNX1 site 1 23 TTTTCAGGAGGAAGCGATGGCTTCAGA 178. RUNX1 site 2 23 TTTCGCTCCGAAGGTAAAAGAAATCAT 179. RUNX1 site 3 23 TTTCAGCCTCACCCCTCTAGCCCTACA 180. RUNX1 site 4 23 TTTCTTCTCCCCTCTGCTGGATACCTC 181. mm: mismatched positions; mismatches which are shown in lower case SpCas9 gRNAs Spacer length Name (nt) Spacer Sequence DNMT1 Spacer length Name (nt) Spacer Sequence DNMT1 site 1 20 GTCACTCTGGGGAACACGCC 182. DNMT1 site 2 20 GAGTGCTAAGGGAACGTTCA 183. DNMT1 site 3 20 GAGACTGAACACTCCTCAAA 184. DNMT1 site 4 20 GGAGTGAGGGAAACGGCCCC 185. SpCas9 gRNAs Spacer length Name (nt) Spacer Sequence EMX1 EMX1 site 1 20 GAGTCCGAGCAGAAGAAGAA 186. EMX1 site 2 20 GTCACCTCCAATGACTAGGG 187. FANCF FANCF site 1 20 GGAATCCCTTCTGCAGCACC 188. FANCF site 2 20 GCTGCAGAAGGGATTCCATG 189. RUNX1 RUNX1 site 1 20 GCATTTTCAGGAGGAAGCGA 190. RUNX1 site 2 20 GGGAGAAGAAAGAGAGATGT 191.

Example 1. Tolerance of AsCpf1 and LbCpf1 to Mismatches in crRNA:Target Site Duplex

In a recent publication (Kleinstiver & Tsai et al., Nature Biotechnology 2016) using 3 different crRNAs targeted to endogenous sites in the human DNMT1 gene, it was determined that both AsCpf1 and LbCpf1 are nearly completely intolerant to pairs of adjacent mismatches in their crRNA:target-site duplex (FIG. 1a ). Compared to the indel formation activity with any of the 3 perfectly matched crRNAs, pairs of mismatches in the crRNA between positions 1/2 to 17/18 nearly completely eliminated detectable indel formation. We also tested the tolerance of both Cpf1s to single mismatches across the length of two different sites and found that AsCpf1 and LbCpf1 could generally discriminate against sites where the crRNA contained a single mismatch at positions 2-6 and 13-17 (FIG. 1b ). Conversely, both Cpf1 orthologues could tolerate single mismatches at positions 1 and 7-12 with varying degrees of efficiency (FIG. 1b ). From both singly- and doubly-mismatched crRNA experiments, it was clear that Cpf1 did not have specificity at positions 18-23 of the spacer and could tolerate single and double mismatches in this region.

More recently, the tolerance of LbCpf1 and AsCpf1 to single mismatches across a third spacer sequence was also examined; while single mismatches at positions 1-4 and 6 abolished cleavage, the remainder of singly-mismatched crRNAs were competent to generate indel mutations with LbCpf1 and AsCpf1 (FIGS. 2A and 2B, respectively).

Overall, these combined experiments demonstrate that although both AsCpf1 and LbCpf1 generally have high genome-wide specificity and can be intolerant to single mismatches across their target site spacer regions, there are a number of positions at which single substitutions are tolerated and could potentially lead to off-target effects. Thus, we were interested in taking a rational approach to engineer high-fidelity Cpf1 (Cpf1-HF) variants that would be unable to tolerate any singly mismatched positions across the entire spacer sequence. These Cpf1-HF variants would be useful for studies that require single-nucleotide resolution in genome-editing applications, such as distinguishing and preferentially editing alleles that differ by a single base change (such as SNPs).

Example 2. Cpf1-HF

A recent crystal structure of AsCpf1 (Yamano et al., Cell 2016) enabled us to look carefully at the 3D-structure of Cpf1 and examine potential amino acid side chains that make non-specific contacts to the DNA backbone (Table 1). We identified a number of AsCpf1 residues whose side-chains appeared to be within contact distance of either the target or non-target DNA strands as candidates to mutate. Similar amino acid positions of LbCpf1 (for which no crystal structure is publicly available) were predicted by generating sequence alignments with AsCpf1 and other Cpf1 orthologues, and then identifying residues that are in homologous positions and contain similar functional groups (Table 1).

TABLE 1 Amino acids of AsCpf1 and LbCpf1 that are predicted to I tried make non-specific contacts to the target and non-target DNA strands Target strand contacts Non-target strand contacts AsCpf1 LbCpf1 (−18)* AsCpf1 LbCpf1 (−18)* N178 N160 K85 K83 S186 S168 K87 R86 N278 N256 R92 K89, K92 N282 N260 N93 N91 R301 K272 R113 N112 T315 S286 K200 R182 S376 K349 R210 K192 N515 D505 K403 K380 R518 R508 K406 R385, R386, K387 N519 N509 Q611 K600 K523 Q513 K613 K601 K524 K514 N647 N607 K603 K591 K653 K614 K780 R737 Q656 K617, N618 Q784 G741 K661 K622 R951 R883 K662 K623 K965 K897 K887 K811 Q1013 K944 R909 R833 Q1014 S945 K1086 K1017 K1017 K948i R1094 K1025, K1026 K1054 K1118 — R1121 K1050 R1127 R1054 R1174 K1096 R1220 — K1288 K1200, K1205 N1291 K1208 *amino acids 1-1228 of SEQ ID NO: 10.

To test the hypothesis of whether alanine substitution of amino acids that potentially make non-specific contacts to the target strand DNA can reduce tolerance of mismatches in the crRNA:target duplex, the activity of multiple LbCpf1 variants was first examined. Using crRNAs that were either matched (for on-target activity) or contained mismatches at positions 8 or 9 (to mimic off-target sites) targeted to DNMT1 sites 1 and 3 (FIGS. 3 and 4, respectively), a number of variants appear to reduce activities with the mismatched crRNAs without dramatic effects on on-target activities.

Given these initial results, it is very likely that combinations of mutations that show improved specificities individually may show even more substantial improvements in specificities. The activities of such variants are examined using an expanded panel of matched and mismatched crRNAs.

Next, to perform an initial screen of AsCpf1 variants whose mutations are homologous to those of the LbCpf1 variants that appeared most promising, the activity of a subset of possible variants was examined using the crRNAs that were matched for DNMT1 site 1 or contained single mismatches at positions 8 or 9 (FIGS. 5A and 5B). A larger number of AsCpf1 variants were tested using crRNAs that were either matched (for on-target activity) or contained mismatches at positions 8 or 9 (to mimic off-target sites) targeted to DNMT1 site 3 (FIG. 6). A number of variants appear to reduce activities with the mismatched crRNAs without dramatic effects on on-target activities. Additional untested mutations and combinations thereof may yield improvements in their abilities to discriminate against mismatched sites.

REFERENCES

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Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

What is claimed is:
 1. An isolated CRISPR from Prevotella and Francisella 1 (Cpf1) protein, wherein the protein is: (a) from Lachnospiraceae bacterium ND2006 (LbCpf1), comprising a sequence that is at least 80% identical to the amino acid sequence of amino acids 19-1246 of SEQ ID NO:1, with mutations at one or more of the following positions: S202, N274, N278, K290, K367, K532, K609, K915, Q962, K963, K966, K1002 and/or S1003 of amino acids 1-1228 of SEQ ID NO:10; or (b) from Acidaminococcus sp. BV3L6 (AsCpf1), comprising a sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:2, with mutations at one or more of the following positions: N178, S186, N278, N282, R301, T315, S376, N515, K523, K524, K603, K965, Q1013, Q1014, and/or K1054 of SEQ ID NO:2.
 2. The isolated protein of claim 1, wherein the protein is LbCpf1 and comprises one or more of the following mutations: S202A, N274A, N278A, K290A, K367A, K532A, K609A, K915A, Q962A, K963A, K966A, K1002A and/or S1003A.
 3. The isolated protein of claim 1, wherein the protein is LbCpf1 and further comprises one or more mutations that decrease nuclease activity selected from the group consisting of mutations at D832 and E925.
 4. The isolated protein of claim 3, wherein the protein is LbCpf1 and comprises mutations D832A and E925A.
 5. The isolated protein of claim 1, wherein the protein is AsCpf1 and comprises one or more of the following mutations: N178A, S186A, N278A, N282A, R301A, T315A, S376A, N515A, K523A, K524A, K603A, K965A, Q1013A, Q1014A, and/or K1054A of SEQ ID NO:2.
 6. The isolated protein of claim 5, wherein the protein is AsCpf1 and further comprises one or more mutations that decrease nuclease activity selected from the group consisting of mutations at D908 and/or E993.
 7. The isolated protein of claim 6, wherein the protein is AsCpf1 and comprising mutations D908A and/or E993A.
 8. A fusion protein comprising the isolated protein of claim 1, fused to a heterologous functional domain, with an optional intervening linker.
 9. The fusion protein of claim 8, wherein the heterologous functional domain is a transcriptional activation domain.
 10. The fusion protein of claim 9, wherein the transcriptional activation domain is from VP64 or NF-κB p65.
 11. The fusion protein of claim 8, wherein the heterologous functional domain is a transcriptional silencer or transcriptional repression domain.
 12. The fusion protein of claim 11, wherein the transcriptional repression domain is a Krueppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3A interaction domain (SID).
 13. The fusion protein of claim 11, wherein the transcriptional silencer is Heterochromatin Protein 1 (HP1).
 14. The fusion protein of claim 8, wherein the heterologous functional domain is an enzyme that modifies the methylation state of DNA.
 15. The fusion protein of claim 14, wherein the enzyme that modifies the methylation state of DNA is a DNA methyltransferase (DNMT) or a TET protein.
 16. The fusion protein of claim 15, wherein the TET protein is TET1.
 17. The fusion protein of claim 10, wherein the heterologous functional domain is an enzyme that modifies a histone subunit.
 18. The fusion protein of claim 8, wherein the enzyme that modifies a histone subunit is a histone acetyltransferase (HAT), histone deacetylase (HDAC), histone methyltransferase (HMT), or histone demethylase.
 19. The fusion protein of claim 8, wherein the heterologous functional domain is a biological tether.
 20. The fusion protein of claim 19, wherein the biological tether is MS2, Csy4 or lambda N protein.
 21. The fusion protein of claim 8, wherein the heterologous functional domain is FokI.
 22. An isolated nucleic acid encoding the protein of claim
 1. 23. A vector comprising the isolated nucleic acid of claim
 22. 24. A host cell, preferably a mammalian host cell, comprising the nucleic acid of claim
 22. 25. A method of altering the genome of a cell, the method comprising expressing in the cell, or contacting the cell with, the isolated protein or fusion protein of claim 1, and a guide RNA having a region complementary to a selected portion of the genome of the cell.
 26. The method of claim 25, wherein the isolated protein or fusion protein comprises one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag.
 27. The method of claim 25, wherein the cell is a stem cell.
 28. The method of claim 27, wherein the cell is an embryonic stem cell, mesenchymal stem cell, or induced pluripotent stem cell; is in a living animal; or is in an embryo.
 29. A method of altering a double stranded DNA (dsDNA) molecule, the method comprising contacting the dsDNA molecule with the isolated protein of claim 1, and a guide RNA having a region complementary to a selected portion of the dsDNA molecule.
 30. The method of claim 29, wherein the dsDNA molecule is in vitro. 